[Bioperl-guts-l] [Bug 2482] New: paml4 mlc file fails to parse

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Apr 7 14:50:15 EDT 2008


http://bugzilla.open-bio.org/show_bug.cgi?id=2482

           Summary: paml4 mlc file fails to parse
           Product: BioPerl
           Version: 1.5 branch
          Platform: Other
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: jayoung at fhcrc.org
                CC: jayoung at fhcrc.org


Hi,

I have just updated our version of PAML to v4, and now have problems parsing
the mlc file with Bio::Tools::Phylo::PAML. 

I think I have also updated to the latest version of bioperl:
$Bio::Tools::Phylo::PAML::VERSION gives 1.0050021

My script is based on  http://bioperl.org/wiki/HOWTO:PAML, and the basics of it
are here:

--------------------

#!/usr/bin/perl

#specify the mlc file(s) on the command line

use Bio::Tools::Phylo::PAML;
use warnings; 
print "PAML version ", $Bio::Tools::Phylo::PAML::VERSION, "\n\n";

foreach my $file (@ARGV) {
my $outcodeml = $file;
if (!-e $outcodeml) {die "\ncan't find the file you specified $outcodeml -
terminating\n\n";}
my $out = "$outcodeml.treeinfo";
print "file $file - output will be in $out\n";
my $paml_parser = new Bio::Tools::Phylo::PAML(-file => $outcodeml,
                                              -dir => "./",
                                              -ctlf => "./codeml.ctl");
open (OUT, "> $out");
print OUT "Descendants\tt\tS\tN\tdN/dS\tdN\tdS\tS*dS\tN*dN\n";
if( my $result = $paml_parser->next_result() ) {
  print "got a result\n"; 
  while ( my $tree = $result->next_tree ) {
     print "found a tree\n";
     my $newtree = new Bio::TreeIO(-file=>'> temp.xml', -format=>'svggraph');
     $newtree->write_tree($tree);
     #do stuff with the tree here.... 
  }
} else {print "no results\n";}

close OUT; 

}

--------------------
It works fine on output from paml 3.15 but on output from paml4 I get the
following:
PAML version 1.0050021
file mlc - output will be in mlc.treeinfo
no results
which tells me that the parser didn't recognize the output. 

I'll attach the mlc file in a few minutes.

thanks in advance for any help,

Janet Young

------------------------------------------------------------------- 

Dr. Janet Young (Trask lab)

Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., C3-168, 
P.O. Box 19024, Seattle, WA 98109-1024, USA.

tel: (206) 667 1471 fax: (206) 667 6524
email: jayoung at fhcrc.org

http://www.fhcrc.org/labs/trask/

-------------------------------------------------------------------


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